feat(index): multi-repo workspaces index as a whole (#514) (#837)

A workspace holding several independent git repos failed two ways:

- Enumeration: a super-repo whose .gitignore hides its child repos
  (/packages/) indexed 0 of their files — git never lists ignored dirs,
  and the #193 embedded-repo recursion only fired for UNTRACKED dirs.
  Gitignored embedded repos are now discovered (ignored-dirs listing +
  bounded .git search) and enumerated by their own git ls-files.
- Change detection: git status in the parent says nothing about embedded
  repos (untracked OR ignored), so codegraph sync missed every child
  change. Status now recurses per embedded repo.

ScopeIgnore is the new single source of truth for indexer + watcher
scope: parent rules for ordinary paths, the child repo's own rules for
paths inside it, built-in defaults uniformly on full paths (a git repo
inside node_modules is an npm git-dependency, not project code), and
ancestors of embedded roots are never pruned (the Linux per-directory
watcher must descend to reach them).

Non-git workspace roots already worked via the per-directory gitignore
walk — locked in by test.

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

CHANGELOG.md

@@ -16,6 +16,8 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### New Features
 
+- **Workspaces holding multiple git repositories now index as a whole.** Running `codegraph init` at the root of a directory that contains several independent git repos — including the common "super-repo" layout where the parent repo's `.gitignore` hides the child repos to keep `git status` quiet — now indexes every nested project into one graph, with each child repo's own `.gitignore` respected. `codegraph sync` and live file watching pick up changes inside the nested repos too (previously change detection only consulted the parent repo, so edits in child repos were invisible until a full re-index). Git repositories inside `node_modules` (npm git-dependencies) remain excluded. (#514)
+
 - **`codegraph_explore` now explains where a flow ends instead of going silent.** When the symbols you ask about don't connect statically — because the code dispatches through a runtime mechanism like a computed call (`handlers[action.type](...)`), Python's `getattr`, a command/mediator bus (`sender.Send(new DeleteCommand(...))`), reflection, or `new Proxy` — explore now announces the exact dispatch site (file and line) where the static path stops, and when the dispatch key is visible in the source it shortlists the likely runtime targets (for example pointing a MediatR command straight at its `Handler.Handle` method). Detection is deterministic and runs only when a flow fails to connect; fully connected flows are unchanged, and nothing about indexing or the graph itself changes. Relatedly, a custom event bus whose emit and handler connect through a single synthesized hop now shows that hop explicitly (with the registration site) — it previously rendered nothing because the connection was "too short" for the flow section. (#687)
 
 - **Anonymous usage telemetry, documented field-by-field and easy to turn off.** CodeGraph now collects a small set of anonymous usage statistics — which commands and MCP tools get used, which languages get indexed, which agents connect — so language and agent support work goes where real usage is. Never any code, file paths, file or symbol names, search queries, or IP addresses; usage aggregates locally into daily totals before anything is sent, and the ingest endpoint is public, auditable code in the repository that enforces the documented field list. The installer asks up front with a visible default-on toggle (and never re-asks); everywhere else a one-line notice prints before the first send. Disable any time with `codegraph telemetry off`, `CODEGRAPH_TELEMETRY=0`, or the cross-tool `DO_NOT_TRACK=1` standard — off means off: nothing is recorded, nothing is sent, and buffered data is deleted. `TELEMETRY.md` documents every field.